Multiple sequence alignment - TraesCS3B01G460400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G460400 chr3B 100.000 5419 0 0 1 5419 704031765 704026347 0.000000e+00 10008.0
1 TraesCS3B01G460400 chr3B 94.682 2708 123 10 1 2701 704126375 704123682 0.000000e+00 4183.0
2 TraesCS3B01G460400 chr3B 97.089 1271 26 3 2707 3977 704123563 704122304 0.000000e+00 2132.0
3 TraesCS3B01G460400 chr3B 96.259 588 22 0 3988 4575 704122321 704121734 0.000000e+00 965.0
4 TraesCS3B01G460400 chr3B 96.107 411 11 1 4610 5015 704119778 704119368 0.000000e+00 665.0
5 TraesCS3B01G460400 chr3B 95.429 350 15 1 354 703 704031296 704030948 1.710000e-154 556.0
6 TraesCS3B01G460400 chr3B 95.429 350 15 1 470 818 704031412 704031063 1.710000e-154 556.0
7 TraesCS3B01G460400 chr3B 94.286 350 17 3 470 818 704126019 704125672 2.870000e-147 532.0
8 TraesCS3B01G460400 chr3B 96.667 300 10 0 5120 5419 704110764 704110465 2.910000e-137 499.0
9 TraesCS3B01G460400 chr3B 91.354 347 18 3 357 703 704125901 704125567 1.060000e-126 464.0
10 TraesCS3B01G460400 chr3B 93.991 233 13 1 355 587 704031179 704030948 8.640000e-93 351.0
11 TraesCS3B01G460400 chr3B 93.991 233 13 1 587 818 704031411 704031179 8.640000e-93 351.0
12 TraesCS3B01G460400 chr3B 93.562 233 13 2 587 818 704126018 704125787 4.020000e-91 346.0
13 TraesCS3B01G460400 chr3B 89.700 233 12 3 355 587 704125787 704125567 2.470000e-73 287.0
14 TraesCS3B01G460400 chr3B 93.043 115 7 1 355 469 704031063 704030950 3.360000e-37 167.0
15 TraesCS3B01G460400 chr3B 93.043 115 7 1 703 816 704031411 704031297 3.360000e-37 167.0
16 TraesCS3B01G460400 chr3B 92.241 116 9 0 703 818 704126018 704125903 1.210000e-36 165.0
17 TraesCS3B01G460400 chr3B 90.476 105 10 0 5012 5116 704119208 704119104 7.320000e-29 139.0
18 TraesCS3B01G460400 chr3B 87.826 115 3 2 355 469 704125672 704125569 2.050000e-24 124.0
19 TraesCS3B01G460400 chr3A 92.736 1886 118 15 940 2813 667138078 667136200 0.000000e+00 2706.0
20 TraesCS3B01G460400 chr3A 91.393 1766 74 13 3025 4787 667136080 667134390 0.000000e+00 2348.0
21 TraesCS3B01G460400 chr3A 94.595 296 13 2 4782 5074 667134205 667133910 6.400000e-124 455.0
22 TraesCS3B01G460400 chr3A 92.446 278 21 0 5142 5419 667133909 667133632 1.090000e-106 398.0
23 TraesCS3B01G460400 chr3A 93.966 116 6 1 2857 2972 667136190 667136076 2.010000e-39 174.0
24 TraesCS3B01G460400 chr3A 83.660 153 14 6 825 974 667200986 667200842 3.410000e-27 134.0
25 TraesCS3B01G460400 chr3A 88.525 61 3 3 914 974 667236894 667236838 2.710000e-08 71.3
26 TraesCS3B01G460400 chr3D 94.301 965 48 4 4460 5419 532107166 532106204 0.000000e+00 1471.0
27 TraesCS3B01G460400 chr3D 92.241 1044 72 9 1773 2813 532114364 532113327 0.000000e+00 1471.0
28 TraesCS3B01G460400 chr3D 92.205 898 36 7 3572 4463 532108094 532107225 0.000000e+00 1240.0
29 TraesCS3B01G460400 chr3D 86.821 1123 79 30 703 1786 532122319 532121227 0.000000e+00 1190.0
30 TraesCS3B01G460400 chr3D 94.627 670 31 3 2911 3576 532110760 532110092 0.000000e+00 1033.0
31 TraesCS3B01G460400 chr3D 79.912 453 38 22 37 469 532122612 532122193 3.200000e-72 283.0
32 TraesCS3B01G460400 chr3D 86.822 129 5 5 587 703 532122319 532122191 3.410000e-27 134.0
33 TraesCS3B01G460400 chr3D 86.154 130 6 5 470 587 532122320 532122191 4.400000e-26 130.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G460400 chr3B 704026347 704031765 5418 True 1736.571429 10008 94.989429 1 5419 7 chr3B.!!$R2 5418
1 TraesCS3B01G460400 chr3B 704119104 704126375 7271 True 909.272727 4183 93.052909 1 5116 11 chr3B.!!$R3 5115
2 TraesCS3B01G460400 chr3A 667133632 667138078 4446 True 1216.200000 2706 93.027200 940 5419 5 chr3A.!!$R3 4479
3 TraesCS3B01G460400 chr3D 532106204 532114364 8160 True 1303.750000 1471 93.343500 1773 5419 4 chr3D.!!$R1 3646
4 TraesCS3B01G460400 chr3D 532121227 532122612 1385 True 434.250000 1190 84.927250 37 1786 4 chr3D.!!$R2 1749

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
268 275 0.107800 GATCTGCTGCCTTCTGCTCA 60.108 55.000 0.00 0.00 42.00 4.26 F
611 637 0.868406 GCATGAGCCATACCTAACGC 59.132 55.000 0.00 0.00 33.58 4.84 F
1207 1241 0.026285 CTTACACTAACATGCGCGCC 59.974 55.000 30.77 11.42 0.00 6.53 F
2084 2139 0.534412 CAGGTGAGGTCGCTCTTGAT 59.466 55.000 0.00 0.00 0.00 2.57 F
2273 2328 1.063174 GGCATGTTGCTAGAGCTTTCG 59.937 52.381 2.72 0.00 44.28 3.46 F
2499 2554 2.198827 TGGACACAGGCCATTTGTAG 57.801 50.000 5.01 0.00 0.00 2.74 F
3854 8544 2.803956 ACTCTCGTGACACTAATGGGA 58.196 47.619 3.68 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1159 1.283613 ACAAAGAAGTCACCCCACACA 59.716 47.619 0.00 0.00 0.00 3.72 R
2084 2139 2.097036 CTTGCAAAGGAGATGGCATCA 58.903 47.619 27.93 3.69 41.27 3.07 R
2926 5602 0.309922 GCCAAGATGATGATGTGGCG 59.690 55.000 1.40 0.00 44.82 5.69 R
3854 8544 1.063792 TGGCTTGCCACATCACCATAT 60.064 47.619 10.65 0.00 0.00 1.78 R
4088 8778 5.416326 CCGTAAAAGGGGTACATTTGATGAA 59.584 40.000 0.00 0.00 0.00 2.57 R
4343 9035 1.005924 CCAAAGGTGTAGGCATCCCTT 59.994 52.381 0.00 0.00 42.87 3.95 R
4760 11444 1.890041 CGCAACCGGTTTCTCCACA 60.890 57.895 19.55 0.00 35.57 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.063510 TGCTTGAGAGAGAACCCAATG 57.936 47.619 0.00 0.00 0.00 2.82
33 34 2.290514 TGCTTGAGAGAGAACCCAATGG 60.291 50.000 0.00 0.00 37.80 3.16
34 35 2.363683 CTTGAGAGAGAACCCAATGGC 58.636 52.381 0.00 0.00 33.59 4.40
35 36 0.250234 TGAGAGAGAACCCAATGGCG 59.750 55.000 0.00 0.00 33.59 5.69
42 46 2.418976 GAGAACCCAATGGCGAAACTAC 59.581 50.000 0.00 0.00 33.59 2.73
48 52 2.416547 CCAATGGCGAAACTACTGACTG 59.583 50.000 0.00 0.00 0.00 3.51
149 153 0.393944 TACAGGATCTGTCGGCGACT 60.394 55.000 36.17 20.05 41.21 4.18
259 266 2.354199 GCTTCTTTACTGATCTGCTGCC 59.646 50.000 0.00 0.00 0.00 4.85
262 269 3.866651 TCTTTACTGATCTGCTGCCTTC 58.133 45.455 0.00 0.00 0.00 3.46
268 275 0.107800 GATCTGCTGCCTTCTGCTCA 60.108 55.000 0.00 0.00 42.00 4.26
280 288 1.748122 CTGCTCAATCGCCAAGCCT 60.748 57.895 0.00 0.00 35.12 4.58
285 293 3.717294 AATCGCCAAGCCTCCGGT 61.717 61.111 0.00 0.00 0.00 5.28
287 295 2.588856 AATCGCCAAGCCTCCGGTAC 62.589 60.000 0.00 0.00 0.00 3.34
378 392 3.643199 TTGCATGAGCCATACCTAACA 57.357 42.857 0.00 0.00 41.13 2.41
386 400 5.433526 TGAGCCATACCTAACACCAAATAC 58.566 41.667 0.00 0.00 0.00 1.89
396 410 5.413523 CCTAACACCAAATACTTAAACGGCT 59.586 40.000 0.00 0.00 0.00 5.52
496 522 2.036733 TGTATGAGCCATACCTAACGCC 59.963 50.000 17.42 0.00 44.11 5.68
524 550 4.613925 TTAAATGGCTGCAATGGTTTGA 57.386 36.364 0.50 0.00 34.60 2.69
544 570 4.308265 TGATACGATGTAGAGAGTCTCGG 58.692 47.826 14.47 4.12 35.36 4.63
556 582 1.153229 GTCTCGGGCCCGCTTAATT 60.153 57.895 39.89 0.00 39.59 1.40
605 631 1.472480 ACGTTTTGCATGAGCCATACC 59.528 47.619 0.00 0.00 41.13 2.73
611 637 0.868406 GCATGAGCCATACCTAACGC 59.132 55.000 0.00 0.00 33.58 4.84
624 650 8.085909 GCCATACCTAACGCCAAATATTTAAAT 58.914 33.333 5.89 5.89 0.00 1.40
627 653 7.412853 ACCTAACGCCAAATATTTAAATGGT 57.587 32.000 11.05 2.20 35.34 3.55
629 655 7.762159 ACCTAACGCCAAATATTTAAATGGTTG 59.238 33.333 11.05 13.07 35.34 3.77
635 661 7.194962 GCCAAATATTTAAATGGTTGCAATGG 58.805 34.615 11.05 1.70 35.34 3.16
661 687 1.956297 ACGATGTAGAGAGTCTCGGG 58.044 55.000 14.47 4.44 35.36 5.14
725 751 4.036734 CGTTTTGCATGAGCCATACCTAAT 59.963 41.667 0.00 0.00 41.13 1.73
751 777 8.039538 TGCCAAATATTTAAACAGATGCAATGA 58.960 29.630 9.10 0.00 0.00 2.57
763 789 5.209977 CAGATGCAATGATTTGGTACGATG 58.790 41.667 0.00 0.00 33.22 3.84
764 790 4.883585 AGATGCAATGATTTGGTACGATGT 59.116 37.500 0.00 0.00 33.22 3.06
765 791 6.018016 CAGATGCAATGATTTGGTACGATGTA 60.018 38.462 0.00 0.00 33.22 2.29
766 792 5.733226 TGCAATGATTTGGTACGATGTAG 57.267 39.130 0.00 0.00 33.22 2.74
767 793 5.423886 TGCAATGATTTGGTACGATGTAGA 58.576 37.500 0.00 0.00 33.22 2.59
768 794 5.523552 TGCAATGATTTGGTACGATGTAGAG 59.476 40.000 0.00 0.00 33.22 2.43
769 795 5.753438 GCAATGATTTGGTACGATGTAGAGA 59.247 40.000 0.00 0.00 33.22 3.10
770 796 6.074088 GCAATGATTTGGTACGATGTAGAGAG 60.074 42.308 0.00 0.00 33.22 3.20
771 797 6.716934 ATGATTTGGTACGATGTAGAGAGT 57.283 37.500 0.00 0.00 0.00 3.24
772 798 6.525578 TGATTTGGTACGATGTAGAGAGTT 57.474 37.500 0.00 0.00 0.00 3.01
813 839 4.157289 AGGCTCATTTGAAGTACTGCAATG 59.843 41.667 17.23 15.82 0.00 2.82
839 865 6.500589 ACCAGTTGATACAACTATAGCCAT 57.499 37.500 15.17 0.00 0.00 4.40
843 869 7.041780 CCAGTTGATACAACTATAGCCATGTTC 60.042 40.741 15.17 9.02 0.00 3.18
884 916 1.350351 GACCCATGCAGCCTCAGATAT 59.650 52.381 0.00 0.00 0.00 1.63
892 924 4.677182 TGCAGCCTCAGATATATCACCTA 58.323 43.478 15.08 0.00 0.00 3.08
893 925 4.708909 TGCAGCCTCAGATATATCACCTAG 59.291 45.833 15.08 6.18 0.00 3.02
900 932 6.889177 CCTCAGATATATCACCTAGAGCAAGA 59.111 42.308 15.08 0.00 0.00 3.02
931 963 3.618351 AGTACCTCACTACGTACAGCAT 58.382 45.455 0.00 0.00 37.83 3.79
1125 1159 0.036858 GCGAGAAGTTTGCTCCCTCT 60.037 55.000 0.00 0.00 33.06 3.69
1207 1241 0.026285 CTTACACTAACATGCGCGCC 59.974 55.000 30.77 11.42 0.00 6.53
1323 1359 8.046708 TGCTACATGTTGATTAATTAGGTCACT 58.953 33.333 11.66 0.00 0.00 3.41
1358 1398 7.781219 ACCATCCATGATCTACATTGAATTTCA 59.219 33.333 0.00 0.00 37.07 2.69
1400 1440 7.924412 ACATGATATAAGTTCATTACGGTCGTT 59.076 33.333 0.00 0.00 31.50 3.85
1467 1517 6.759497 AAATAGGCTACATGAAACTTCACC 57.241 37.500 0.00 0.00 40.49 4.02
1492 1542 5.711698 AGGAAGTTCCTTTTTGTGGGATAA 58.288 37.500 19.27 0.00 46.91 1.75
1536 1586 1.399440 CCTGCACGATTGACATCCAAG 59.601 52.381 0.00 0.00 38.31 3.61
1649 1701 2.401766 GCAAGGACGCCATGACTGG 61.402 63.158 0.00 0.00 46.17 4.00
1901 1956 7.829725 TGAATCAAGCTGTGTTATTTTAGCAT 58.170 30.769 0.00 0.00 38.59 3.79
1957 2012 7.778083 AGATATGTTTGAATCAATGTGCATGT 58.222 30.769 0.00 0.00 0.00 3.21
2084 2139 0.534412 CAGGTGAGGTCGCTCTTGAT 59.466 55.000 0.00 0.00 0.00 2.57
2273 2328 1.063174 GGCATGTTGCTAGAGCTTTCG 59.937 52.381 2.72 0.00 44.28 3.46
2292 2347 2.631062 TCGAGGCTGAACTTTAACCTCA 59.369 45.455 8.00 0.00 45.95 3.86
2411 2466 8.714179 TCTTCACTATAATAAAACCAACACGTG 58.286 33.333 15.48 15.48 0.00 4.49
2499 2554 2.198827 TGGACACAGGCCATTTGTAG 57.801 50.000 5.01 0.00 0.00 2.74
2519 2574 4.408182 AGTGTGCCATATTGTCTCCTAC 57.592 45.455 0.00 0.00 0.00 3.18
2521 2576 3.134804 GTGTGCCATATTGTCTCCTACCT 59.865 47.826 0.00 0.00 0.00 3.08
2523 2578 4.141711 TGTGCCATATTGTCTCCTACCTTC 60.142 45.833 0.00 0.00 0.00 3.46
2662 2718 7.353414 TGATTTTGACATTGGTTTTGGAGTA 57.647 32.000 0.00 0.00 0.00 2.59
2666 2722 4.798882 TGACATTGGTTTTGGAGTAACCT 58.201 39.130 0.00 0.00 44.32 3.50
2798 2971 4.082517 GCATTGAAAAGGGAAAGGACTCTC 60.083 45.833 0.00 0.00 0.00 3.20
2820 2993 4.384547 TCGAGACAATTGAATACACACACG 59.615 41.667 13.59 3.59 0.00 4.49
3342 6020 7.222999 GCAATGCAAAGGTAGACTACTAGTTAG 59.777 40.741 12.31 0.00 0.00 2.34
3430 6117 8.588472 TGATCTCTAATGGGTATCATTGTACTG 58.412 37.037 0.00 0.00 45.00 2.74
3854 8544 2.803956 ACTCTCGTGACACTAATGGGA 58.196 47.619 3.68 0.00 0.00 4.37
4389 9081 1.263356 CCTAAAGGACCTCGTCACCA 58.737 55.000 0.00 0.00 37.39 4.17
4397 9089 1.068741 GACCTCGTCACCACACTCTTT 59.931 52.381 0.00 0.00 32.09 2.52
4686 11369 5.946377 AGTTCATCCCTTTAAAGTGTCATCC 59.054 40.000 14.03 0.00 0.00 3.51
4760 11444 0.896940 CCTGGAGTGCTGCCAAATGT 60.897 55.000 0.00 0.00 34.44 2.71
4836 11710 5.994054 GGTATGCATATCTCTTTTGCTCTCA 59.006 40.000 10.16 0.00 37.28 3.27
5158 12200 6.288294 ACTGTAGATGTTAGTGTCTTGCAAA 58.712 36.000 0.00 0.00 0.00 3.68
5272 12315 4.097892 ACAGAAAGACATCGGCAAGTTTTT 59.902 37.500 0.00 0.00 0.00 1.94
5310 12353 8.259872 CGAATACTACGATGTACACAAGAAATG 58.740 37.037 0.00 0.00 0.00 2.32
5313 12356 4.668576 ACGATGTACACAAGAAATGCTG 57.331 40.909 0.00 0.00 0.00 4.41
5316 12359 3.624326 TGTACACAAGAAATGCTGCAC 57.376 42.857 3.57 0.00 0.00 4.57
5361 12404 6.403636 GCACTGTATCCAAACCTGAAACTATG 60.404 42.308 0.00 0.00 0.00 2.23
5372 12415 6.368779 ACCTGAAACTATGGTAACTAGCAA 57.631 37.500 0.00 0.00 37.24 3.91
5380 12423 6.341316 ACTATGGTAACTAGCAATGTGTCTG 58.659 40.000 0.00 0.00 37.24 3.51
5404 12447 1.831736 ACCAGAAACTATGACTCCGGG 59.168 52.381 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.627329 TCTCTCTCAAGCAAGCCACAT 59.373 47.619 0.00 0.00 0.00 3.21
32 33 4.806342 TTTTTCAGTCAGTAGTTTCGCC 57.194 40.909 0.00 0.00 0.00 5.54
101 105 2.051692 TCCCCCATTAACATAGACGGG 58.948 52.381 0.00 0.00 0.00 5.28
149 153 6.169557 ACTATGCATCGTTTTCCCTATACA 57.830 37.500 0.19 0.00 0.00 2.29
259 266 0.098376 GCTTGGCGATTGAGCAGAAG 59.902 55.000 0.00 0.00 39.27 2.85
262 269 1.712977 GAGGCTTGGCGATTGAGCAG 61.713 60.000 0.00 0.00 38.14 4.24
280 288 2.048023 CCACGTAGCCTGTACCGGA 61.048 63.158 9.46 0.00 0.00 5.14
285 293 1.407618 CATGTAGCCACGTAGCCTGTA 59.592 52.381 1.24 0.00 0.00 2.74
287 295 1.154205 GCATGTAGCCACGTAGCCTG 61.154 60.000 1.24 0.00 37.23 4.85
378 392 3.150767 TGCAGCCGTTTAAGTATTTGGT 58.849 40.909 0.00 0.00 0.00 3.67
386 400 2.723124 AACCATTGCAGCCGTTTAAG 57.277 45.000 0.00 0.00 0.00 1.85
396 410 2.509569 ACATCGTACCAAACCATTGCA 58.490 42.857 0.00 0.00 35.10 4.08
469 495 2.943033 AGGTATGGCTCATACAAAACGC 59.057 45.455 20.13 7.70 45.86 4.84
471 497 5.503520 GCGTTAGGTATGGCTCATACAAAAC 60.504 44.000 20.13 19.46 45.86 2.43
477 503 2.321719 TGGCGTTAGGTATGGCTCATA 58.678 47.619 0.00 0.00 39.03 2.15
496 522 7.556733 ACCATTGCAGCCATTTAAATATTTG 57.443 32.000 11.05 1.13 0.00 2.32
524 550 3.666274 CCCGAGACTCTCTACATCGTAT 58.334 50.000 4.52 0.00 0.00 3.06
544 570 2.290071 TGAGCCTATAATTAAGCGGGCC 60.290 50.000 13.81 0.00 40.32 5.80
556 582 6.233905 TGCAGTACTTCAAATGAGCCTATA 57.766 37.500 0.00 0.00 0.00 1.31
605 631 7.276658 TGCAACCATTTAAATATTTGGCGTTAG 59.723 33.333 11.05 0.00 32.26 2.34
611 637 8.278729 ACCATTGCAACCATTTAAATATTTGG 57.721 30.769 11.05 6.65 35.31 3.28
624 650 1.338337 CGTACCAAACCATTGCAACCA 59.662 47.619 0.00 0.00 35.10 3.67
627 653 2.887783 ACATCGTACCAAACCATTGCAA 59.112 40.909 0.00 0.00 35.10 4.08
629 655 3.936453 TCTACATCGTACCAAACCATTGC 59.064 43.478 0.00 0.00 35.10 3.56
635 661 5.564048 AGACTCTCTACATCGTACCAAAC 57.436 43.478 0.00 0.00 0.00 2.93
661 687 3.053831 TGAGCCTATAATTAAGCGGGC 57.946 47.619 11.09 11.09 39.82 6.13
725 751 8.039538 TCATTGCATCTGTTTAAATATTTGGCA 58.960 29.630 11.05 6.08 0.00 4.92
741 767 4.883585 ACATCGTACCAAATCATTGCATCT 59.116 37.500 0.00 0.00 35.10 2.90
743 769 6.054941 TCTACATCGTACCAAATCATTGCAT 58.945 36.000 0.00 0.00 35.10 3.96
751 777 6.106673 CCAAACTCTCTACATCGTACCAAAT 58.893 40.000 0.00 0.00 0.00 2.32
763 789 1.449778 GCGGGCCCAAACTCTCTAC 60.450 63.158 24.92 0.00 0.00 2.59
764 790 1.198759 AAGCGGGCCCAAACTCTCTA 61.199 55.000 24.92 0.00 0.00 2.43
765 791 1.198759 TAAGCGGGCCCAAACTCTCT 61.199 55.000 24.92 3.49 0.00 3.10
766 792 0.322187 TTAAGCGGGCCCAAACTCTC 60.322 55.000 24.92 0.73 0.00 3.20
767 793 0.331616 ATTAAGCGGGCCCAAACTCT 59.668 50.000 24.92 7.15 0.00 3.24
768 794 1.182667 AATTAAGCGGGCCCAAACTC 58.817 50.000 24.92 4.65 0.00 3.01
769 795 2.517998 TAATTAAGCGGGCCCAAACT 57.482 45.000 24.92 13.34 0.00 2.66
770 796 3.254903 CCTATAATTAAGCGGGCCCAAAC 59.745 47.826 24.92 10.85 0.00 2.93
771 797 3.492337 CCTATAATTAAGCGGGCCCAAA 58.508 45.455 24.92 10.56 0.00 3.28
772 798 2.816337 GCCTATAATTAAGCGGGCCCAA 60.816 50.000 24.92 8.97 34.19 4.12
813 839 5.007724 GGCTATAGTTGTATCAACTGGTTGC 59.992 44.000 20.71 18.89 40.24 4.17
839 865 9.955102 TCTCTATTTATAGACCTATAGCGAACA 57.045 33.333 0.00 0.00 35.64 3.18
869 901 4.102598 AGGTGATATATCTGAGGCTGCAT 58.897 43.478 13.79 0.00 0.00 3.96
928 960 8.514136 TTGCAAATACTTGTAACAACTAATGC 57.486 30.769 0.00 0.00 32.90 3.56
986 1018 1.403249 GCGCCATTCAAAGCTTGATGT 60.403 47.619 0.00 0.00 39.84 3.06
989 1023 1.586028 GGCGCCATTCAAAGCTTGA 59.414 52.632 24.80 0.00 38.04 3.02
992 1026 2.036256 AGGGCGCCATTCAAAGCT 59.964 55.556 30.85 10.59 0.00 3.74
993 1027 2.491621 GAGGGCGCCATTCAAAGC 59.508 61.111 30.85 8.01 0.00 3.51
1047 1081 2.819595 CCATCGGCCTTGGTCACG 60.820 66.667 12.35 0.00 0.00 4.35
1070 1104 4.935495 CGGCCACCTGCACAGTGT 62.935 66.667 2.24 0.00 43.89 3.55
1098 1132 4.440250 GGAGCAAACTTCTCGCTAGTATCA 60.440 45.833 0.00 0.00 35.75 2.15
1125 1159 1.283613 ACAAAGAAGTCACCCCACACA 59.716 47.619 0.00 0.00 0.00 3.72
1207 1241 9.939047 GAAAGATAATGCATATAGTTAACGTCG 57.061 33.333 0.00 0.00 0.00 5.12
1383 1423 3.389925 TCCAACGACCGTAATGAACTT 57.610 42.857 0.00 0.00 0.00 2.66
1400 1440 1.982660 TTGCGTGGTATTTGGTTCCA 58.017 45.000 0.00 0.00 0.00 3.53
1492 1542 9.990868 AGGTAGGATAAAATCATTAACTTGGTT 57.009 29.630 0.00 0.00 0.00 3.67
1536 1586 8.723942 TCTGCTAGAAAGAACTCAATTAATCC 57.276 34.615 0.00 0.00 0.00 3.01
1649 1701 3.185188 CACATATGTTAGTGCATCGGCTC 59.815 47.826 5.37 0.00 41.91 4.70
1901 1956 2.877786 ACGTGACATGCATGTTTTGAGA 59.122 40.909 31.82 10.47 44.17 3.27
2084 2139 2.097036 CTTGCAAAGGAGATGGCATCA 58.903 47.619 27.93 3.69 41.27 3.07
2273 2328 5.586643 CCTAATGAGGTTAAAGTTCAGCCTC 59.413 44.000 1.93 1.93 44.31 4.70
2292 2347 4.635473 TCCTTGAGGTGAAGGATCCTAAT 58.365 43.478 16.55 0.00 45.52 1.73
2355 2410 9.362151 AGGGTAAACATCAATGAGAAAAGTTTA 57.638 29.630 0.00 0.00 34.15 2.01
2356 2411 8.250143 AGGGTAAACATCAATGAGAAAAGTTT 57.750 30.769 0.00 0.00 35.44 2.66
2519 2574 7.512992 AGATCCTAAATGACAATACTGGAAGG 58.487 38.462 0.00 0.00 39.30 3.46
2523 2578 9.057089 GGTAAAGATCCTAAATGACAATACTGG 57.943 37.037 0.00 0.00 0.00 4.00
2666 2722 3.428725 GCACATGAAAGACAACCACAACA 60.429 43.478 0.00 0.00 0.00 3.33
2798 2971 4.628081 CGTGTGTGTATTCAATTGTCTCG 58.372 43.478 5.13 0.00 0.00 4.04
2855 3028 7.936950 TCATAGCAAGAGTTATTGATTCTCG 57.063 36.000 0.00 0.00 33.96 4.04
2926 5602 0.309922 GCCAAGATGATGATGTGGCG 59.690 55.000 1.40 0.00 44.82 5.69
3042 5720 4.879598 ACCGATGACGTTTCTACTTCTTT 58.120 39.130 0.00 0.00 37.88 2.52
3430 6117 7.872993 TCATTTTCATCCCATCTACGAATAGAC 59.127 37.037 0.00 0.00 40.32 2.59
3854 8544 1.063792 TGGCTTGCCACATCACCATAT 60.064 47.619 10.65 0.00 0.00 1.78
3986 8676 9.244292 TGTTTGCCAACATATATACCTTGTAAA 57.756 29.630 0.00 0.00 38.03 2.01
3987 8677 8.809468 TGTTTGCCAACATATATACCTTGTAA 57.191 30.769 0.00 0.00 38.03 2.41
3988 8678 8.809468 TTGTTTGCCAACATATATACCTTGTA 57.191 30.769 3.93 0.00 42.66 2.41
3989 8679 7.710676 TTGTTTGCCAACATATATACCTTGT 57.289 32.000 3.93 0.00 42.66 3.16
3990 8680 8.994429 TTTTGTTTGCCAACATATATACCTTG 57.006 30.769 3.93 0.00 42.66 3.61
3997 8687 9.764363 TGTGTTTATTTTGTTTGCCAACATATA 57.236 25.926 3.93 3.58 42.66 0.86
3998 8688 8.668510 TGTGTTTATTTTGTTTGCCAACATAT 57.331 26.923 3.93 4.46 42.66 1.78
3999 8689 8.492673 TTGTGTTTATTTTGTTTGCCAACATA 57.507 26.923 3.93 0.00 42.66 2.29
4000 8690 6.992063 TGTGTTTATTTTGTTTGCCAACAT 57.008 29.167 3.93 0.00 42.66 2.71
4001 8691 6.428159 ACTTGTGTTTATTTTGTTTGCCAACA 59.572 30.769 0.00 0.00 41.39 3.33
4088 8778 5.416326 CCGTAAAAGGGGTACATTTGATGAA 59.584 40.000 0.00 0.00 0.00 2.57
4293 8985 1.526575 GCCATGTTCACCACCACCTG 61.527 60.000 0.00 0.00 0.00 4.00
4343 9035 1.005924 CCAAAGGTGTAGGCATCCCTT 59.994 52.381 0.00 0.00 42.87 3.95
4389 9081 3.056035 GGTACCGGATTGAGAAAGAGTGT 60.056 47.826 9.46 0.00 0.00 3.55
4731 11415 2.203788 ACTCCAGGTTCGGCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
4760 11444 1.890041 CGCAACCGGTTTCTCCACA 60.890 57.895 19.55 0.00 35.57 4.17
4836 11710 6.069905 TGGGGTACATGACTGTATACACAAAT 60.070 38.462 0.08 0.00 39.93 2.32
5158 12200 6.803320 CGTCAAATCTGTAATCAGTGCATTTT 59.197 34.615 0.00 0.00 41.91 1.82
5272 12315 8.248253 ACATCGTAGTATTCGATATAATGCCAA 58.752 33.333 0.70 0.00 44.49 4.52
5285 12328 8.056571 GCATTTCTTGTGTACATCGTAGTATTC 58.943 37.037 0.00 0.00 0.00 1.75
5292 12335 3.120199 GCAGCATTTCTTGTGTACATCGT 60.120 43.478 0.00 0.00 0.00 3.73
5310 12353 2.213499 AGAACAGTTGTACAGTGCAGC 58.787 47.619 7.11 0.00 0.00 5.25
5313 12356 5.118817 GCTAGTTAGAACAGTTGTACAGTGC 59.881 44.000 7.11 0.00 0.00 4.40
5316 12359 6.363626 CAGTGCTAGTTAGAACAGTTGTACAG 59.636 42.308 0.00 0.00 34.12 2.74
5361 12404 3.334691 TGCAGACACATTGCTAGTTACC 58.665 45.455 0.00 0.00 42.02 2.85
5372 12415 3.290710 AGTTTCTGGTTTGCAGACACAT 58.709 40.909 9.87 0.00 33.25 3.21
5380 12423 3.125316 CGGAGTCATAGTTTCTGGTTTGC 59.875 47.826 0.00 0.00 0.00 3.68


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.